Molecular Evolutionary Analysis of the Thiamine-Diphosphate-Dependent Enzyme, Transketolase

Members of the transketolase group of thiamine- diphosphate-dependent enzymes from 17 different organisms including mammals, yeast, bacteria, and plants have been used for phylogenetic reconstruction. Alignment of the amino acid and DNA sequences for 21 transketolase enzymes and one putative transketolase reveals a number of highly conserved regions and invariant residues that are of predicted importance for enzyme activity, based on the crystal structure of yeast transketolase. One particular sequence of 36 residues has some similarities to the nucleotide-binding motif and we designate it as the transketolase motif. We report further evidence that the recP protein from Streptococcus pneumoniae might be a transketolase and we list a number of invariant residues which might be involved in substrate binding. Phylogenies derived from the nucleotide and the amino acid sequences by various methods show a conventional clustering for mammalian, plant, and gramnegative bacterial transketolases. The branching order of the gram-positive bacteria could not be inferred reliably. The formaldehyde transketolase (sometimes known as dihydroxyacetone synthase) of the yeast Hansenula polymorpha appears to be orthologous to the mammalian enzymes but paralogous to the other yeast transketolases. The occurrence of more than one transketolase gene in some organisms is consistent with several gene duplications. The high degree of similarity in functionally important residues and the fact that the same kinetic mechanism is applicable to all characterized transketolase enzymes is consistent with the proposition that they are all derived from one common ancestral gene. Transketolase appears to be an ancient enzyme that has evolved slowly and might serve as a model for a molecular clock, at least within the mammalian clade

Molecular Evolutionary Analysis of the Thiamine-Diphosphate-Dependent Enzyme, Transketolase

Members of the transketolase group of thiamine- diphosphate-dependent enzymes from 17 different organisms including mammals, yeast, bacteria, and plants have been used for phylogenetic reconstruction. Alignment of the amino acid and DNA sequences for 21 transketolase enzymes and one putative transketolase reveals a number of highly conserved regions and invariant residues that are of predicted importance for enzyme activity, based on the crystal structure of yeast transketolase. One particular sequence of 36 residues has some similarities to the nucleotide-binding motif and we designate it as the transketolase motif. We report further evidence that the recP protein from Streptococcus pneumoniae might be a transketolase and we list a number of invariant residues which might be involved in substrate binding. Phylogenies derived from the nucleotide and the amino acid sequences by various methods show a conventional clustering for mammalian, plant, and gramnegative bacterial transketolases. The branching order of the gram-positive bacteria could not be inferred reliably. The formaldehyde transketolase (sometimes known as dihydroxyacetone synthase) of the yeast Hansenula polymorpha appears to be orthologous to the mammalian enzymes but paralogous to the other yeast transketolases. The occurrence of more than one transketolase gene in some organisms is consistent with several gene duplications. The high degree of similarity in functionally important residues and the fact that the same kinetic mechanism is applicable to all characterized transketolase enzymes is consistent with the proposition that they are all derived from one common ancestral gene. Transketolase appears to be an ancient enzyme that has evolved slowly and might serve as a model for a molecular clock, at least within the mammalian clade

Genetic association study of UCMA/GRP and OPTN genes (PDB6 locus) with Paget's disease of bone

We performed a genetic association study of rare variants and single nucleotide polymorphisms (SNPs) of UCMA/GRP and OPTN genes, in French-Canadian patients with Paget's disease of bone (PDB) and in healthy controls from the same population. We reproduced the variant found in the UCMA/GRP basal promoter and tested its functionality using in vitro transient transfection assays. Interestingly, this SNP rs17152980 appears to affect the transcription level of UCMA/GRP. In addition, we have identified five rare genetic variants in UCMA/GRP gene, four of them being population-specific, although none were found to be associated with PDB. Six Tag SNPs of UCMA/GRP gene were associated with PDB, particularly the SNP rs17152980 (uncorrected P = 3.8 x 10(-3)), although not significant after Bonferroni's correction. More importantly, we replicated the strong and statistically significant genetic association of two SNPs of the OPTN gene, the rs1561570 (uncorrected P = 5.7 x 10(-7)) and the rs2095388 (uncorrected P = 4.9 x 10(-3)), With PDB. In addition, we identified a very rare variant found to be located close to the basal promoter of the OPTN gene, at -232 bp from its distal transcription start site. Furthermore, depending on the type of allele present (G or A), the binding of several important nuclear factors such as the vitamin D or the retinoic acid receptors is predicted to be altered at this position, suggesting a significant effect in the regulation of transcription of the OPTN gene. In conclusion, we identified a functional SNP located in the basal promoter of the UCMA/GRP gene which provided a weak genetic association with PDB. In addition, we replicated the strong genetic association of two already known SNPs of the OPTN gene, with PDB in a founder effect population. We also identified a very rare variant in the promoter of OPTN, and through bioinformatic analysis, identified putative transcription factor binding sites likely to affect OPTN gene transcription. (C) 2012 Elsevier Inc. All rights reserved.Fonds de la Recherche du Quebec - Sante (FRQS), Canada; Portuguese Science and Technology Foundation, Portugal [SFRH/BPD/48206/2008]; Catalyst Grant (Bone Health) from the Canadian Institutes of Health Research (Canada); CHUQ Foundation (Canada); Groupe de Recherche en Maladies Osseuses (Canada); Canadian Foundation for Innovation (Canada); FRSQ (Canada); Laval University (Canada); CHUQ (CHUL) Research Centre (Canada); Centre of Marine Sciences (CCMAR) (Portugal)info:eu-repo/semantics/publishedVersio

Magneto-structural correlations in arsenic- and selenium-ligated dysprosium single-molecule magnets

The structures and magnetic properties of the arsenic- and selenium-ligated dysprosium single-molecule magnets (SMMs) [Cp'3Dy(AsH2Mes)] (3-Dy), [(h5-Cp02Dy){m-As(H)Mes}]3 (4-Dy), [Li(thf)4]2[(h5-Cp02Dy)3(m3-AsMes)3Li] ([Li(thf)4]2[5-Dy]), and [(h5-Cp02Dy){m-SeMes}]3 (6-Dy) are described. The arsenic-ligated complexes 4-Dy and 5-Dy are the first SMMs to feature ligands with metalloid elements as the donor atoms. The arsenide-ligated complex 4-Dy and the selenolate-ligated complex 6-Dy show large anisotropy barriers in the region of 250 cm�1 in zero d.c. field, increasing to 300 cm�1 upon 5% magnetic dilution. Theoretical studies reveal that thermal relaxation in these SMMs occurs via the second-excited Kramers' doublet. In contrast, the arsinidene-ligated SMM 5-Dy gives a much smaller barrier of 23 cm�1, increasing to 35 cm�1 upon dilution. The field-dependence of the magnetization for 4-Dy and 5-Dy at 1.8 K show unusual plateaus around 10 kOe, which is due to the dominance of arsenic-mediated exchange over the dipolar exchange. The effects of the exchange interactions are more pronounced in 5-Dy, which is a consequence of a small but significant increase in the covalent contribution to the predominantly ionic dysprosium-arsenic bonds. Whereas the magnetically non-dilute dysprosium SMMs show only very narrow magnetization versus field hysteresis loops at 1.8 K, the impact of magnetic dilution is dramatic, with butterfly-shaped loops being observed up to 5.4 K in the case of 4-Dy. Our findings suggest that ligands with heavier p-block element donor atoms have considerable potential to be developed more widely for applications in molecular magnetism

Utilization of ancillary studies in the cytologic diagnosis of respiratory lesions: The papanicolaou society of cytopathology consensus recommendations for respiratory cytology

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134863/1/dc23549.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134863/2/dc23549_am.pd

Committee II: Guidelines for cytologic sampling techniques of lung and mediastinal lymph nodes

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146505/1/dc23975.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146505/2/dc23975_am.pd

Magnetic Slow Relaxation in a Metal–Organic Framework Made of Chains of Ferromagnetically Coupled Single-Molecule Magnets

International audienceWe report the study of a Dy-based metal-organic framework (MOF) with unprecedented magnetic properties. The compound is made of nine-coordinated Dy-III magnetic building blocks (MBBs) with poor intrinsic single-molecule magnet behavior. However, the MOF architecture constrains the MBBs in a one-dimensional structure that induces a ferromagnetic coupling between them. Overall, the material shows a magnetic slow relaxation in absence of external static field and a hysteretic behavior at 0.5K. Low-temperature magnetic studies, diamagnetic doping, and ab initio calculations highlight the crucial role played by the Dy-Dy ferromagnetic interaction. Overall, we report an original magnetic object at the frontier between single-chain magnets and single-molecule magnets that host intrachain couplings that cancel quantum tunneling between the MBBs. This compound is evidence that a bottom-up approach through MOF design can induce spontaneous organization of MBBs able to produce remarkable molecular magnetic materials

Single molecule magnetic behaviour in lanthanide naphthalenesulfonate complexes

The use of 2-naphthalenesulfonate (NAS) ligand in lanthanide chemistry afforded a family of isostructural mononuclear lanthanide complexes with formula [Ln(NAS)2(H2O)6](NAS)·3H2O [Ln = Tb (1), Dy (2), Er (3), Yb (4)]. Crystallographic studies determine a square antiprismatic geometry (D4d) for the Ln centre and crystallization in unprecedented chiral space group. The latter was further confirmed by the observation of Cotton effects in single crystal circular dichroism (CD) spectra. Static and dynamic magnetic measurements identify weak intermolecular dipolar interactions in 2, and such effects can be waived by dilution, which was noted by the detection of zero-field single molecule magnet (SMM) behaviour and hysteresis loop in the magnetically diluted sample (5). Compounds 2-4 exhibit SMM behaviours with energy barriers of 53, 32 and 45 K, respectively. To the best of our knowledge, these complexes provide the first examples of pure 4f sulfonate-based SMMs

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field